Tropical Storm Francisco and Typhoon Lekima are not expected to hit the country's main island, but heavy rains and strong winds are anticipated to disrupt coastal infrastructure and services.
Last week Typhoon Wipha killed 30 people and left 15 missing on the island of 8,500, local media reported.
Footage filmed by Japanese broadcaster TV Tokyo showed elderly islanders preparing to evacuate on Thursday.
"I'm worried, but I heard what everyone's saying so I'm leaving the island," one unidentified resident said.
The latest storms are expected to skirt Japan's main island, but buffet Tokyo with rain and wind.
On Izu Oshima island, 74.5 miles south of Tokyo, officials have asked more than 500 people to evacuate.
The island bore the brunt of the damage from Typhoon Wipha as it swept up the Japanese coast and efforts to clear up the debris are still underway